Nothing
#' Show a three- or two-dimensional plot of a prcomp object
#'
#' Show a three- two-dimensional plot of a prcomp object or a matrix, using
#' different symbols and colors for groups of data
#'
#' The pca3d function shows a three dimensional representation of a PCA object or any
#' other matrix. It uses the rgl package for rendering.
#'
#' pca2d is the 2D counterpart. It creates a regular, two-dimensional plot
#' on the standard graphic device. However, it takes exactly the same
#' options as pca3d, such that it is easy to create 2D variants of the 3D
#' graph.
#'
#' Often, PCA visualisation requires using different symbols and colors for
#' different groups of data. pca3d() and pca2d() aim at creating reasonable
#' defaults, such that a simple call with two parameters -- the pca object
#' and the vector with group assignments of the samples -- is sufficient for
#' a basic diagnosis.
#'
#' @section Biplots:
#'
#' If option \option{biplot} is TRUE, a biplot showing both the PCA results
#' (samples) and variables is shown. This corresponds to the
#' \code{\link{biplot}} function which works for the \code{\link{prcomp}}
#' class objects. However, a biplot showing all variable loadings will be
#' unreadable if the data is highly dimensional (for example, gene
#' expression data). Therefore, the option \option{biplot.vars} specifies
#' which variables are shown on the biplot.
#'
#' If \option{biplot.vars} is a vector of length larger than one, it will be
#' interpreted as a direct selection of the variables to be shown; for
#' example, for a \code{\link{prcomp}} object \var{pca}, the variable selection will
#' happen through \code{pca$rotation[biplot.vars,]}.
#'
#' If \option{biplot.vars} is a single number, then for each of the
#' components shown, a number of variables equal to \option{biplot.vars}
#' with the highest absolute loadings will be shown on the biplot.
#'
#' @param pca
#' Either a prcomp object or a matrix with at least three columns
#' @param components
#' Vector of length 3 (\code{pca3d}) or 2 (\code{pca2d}) containing the components to be shown
#' @param col
#' Either a single value or a vector of length equal to number of rows,
#' containing color definitions for the plot points to be shown
#' @param title
#' Window title
#' @param new
#' Use TRUE to open a new window
#' @param axes.color
#' Axis color
#' This option has no effect in pca2d.
#' @param bg
#' Background color
#' @param palette
#' Specifies the color palette when colors are automatically assigned to
#' the groups. See Details.
#' @param fancy
#' set \option{show.labels}, \option{show.shadows},
#' \option{show.centroids} and \option{show.group.labels} to TRUE.
#' @param radius
#' Scaling item for the size of points to be shown.
#' In pca2d, this corresponds to the cex parameter.
#' @param biplot
#' Specify whether to show a biplot (see section \sQuote{biplots} below)
#' @param biplot.vars
#' Specify which loading to show on the biplot (see section
#' \sQuote{biplots} below)
#' @param legend
#' If NULL, no legend will be drawn. Otherwise the value specifies the
#' legend position in a form accepted by \code{\link{legend}} and \code{\link{legend3d}}.
#' @param group
#' either NULL or a factor of length equal to number of rows. Factor levels
#' can be used to automatically generate symbols and colors for the points
#' shown
#' @param shape
#' Either a single value or a character vector describing the shapes to be
#' used when drawing data points. Allowed shapes are: sphere, tetrahaedron
#' and cube, and may be abbreviated.
#' In pca2d, the parameter is passed directly on to the pch option of the
#' points() function.
#' @param show.labels
#' TRUE for showing labels (taken from the coordinate matrix or the prcomp
#' object). Alternatively, a vector with labels to be shown next to the data
#' points.
#' @param labels.col
#' Single value or vector describing the colors of the labels.
#' @param show.scale
#' TRUE for showing a numeric scale at the edges of the plot.
#' This option has no effect in pca2d.
#' @param show.axes
#' TRUE to show the axes.
#' This option has no effect in pca2d.
#' @param show.axe.titles
#' If TRUE, show axe titles (PC 1, PC 2 etc.)
#' This option has no effect in pca2d.
#' @param axe.titles
#' A vector with two (pca2d) or three (pca3d) values containing the axe
#' titles (corresponds to xlab and ylab in regular plot). If missing, but
#' show.axe.titles is TRUE, axe titles will be generated automatically.
#' @param show.plane
#' If TRUE, show a grey horizontal plane at y = 0.
#' This option has no effect in pca2d.
#' @param show.shadows
#' If TRUE, show a "lollipop" representation of the points on the y = 0
#' plane: a vertical line joining the data point with the plane and a
#' shadow.
#' In pca2d, for each sample at (x,y), a grey line is drawn from (x,y) to
#' (x,0).
#' @param show.centroids
#' If TRUE and the group variable is defined, show cluster centroids (using
#' apropriate group symbols) and lines from each data point to the
#' corresponding centroid.
#' @param show.group.labels
#' Either TRUTH/FALSE or a vector equal to the number of unique values in
#' the \code{group} parameter. If set, labels for each of the defined
#' group will be shown at the group's centroid. If the value of the
#' parameter is TRUE, then the group names will be taken from the
#' \code{group} parameter. Otherwise, the values from this parameter will
#' be used.
#' @param show.shapes
#' A TRUTH/FALSE value indicating whether the different symbols (shapes)
#' for the shown data points should be plotted (default TRUE).
#' @param show.ellipses
#' A TRUTH/FALSE value indicating whether to show confidence interval ellipses or
#' ellipsoids around each defined group
#' @param ellipse.ci
#' The confidence level of a pairwise confidence region for the CI. The
#' default is 0.95, for a 95% region. This is used to control
#' the size of the ellipse being plotted.
#' @param ...
#' For pca2d, any further argument will be passed on to the points()
#' function.
#' @return Both pca2d and pca3d return invisibly a data frame which can be used to generate
#' a legend for the figure. The data frame has as many rows as there are
#' groups, and column with the group name, assigned color and assigned shape.
#' @examples
#' data( metabo )
#' pca <- prcomp( metabo[,-1], scale.= TRUE )
#'
#' pca3d( pca, group= metabo[,1] )
#' pca2d( pca, group= metabo[,1] )
#'
#' ## a bit more fancy:
#' ## black background, white axes,
#' ## centroids
#' pca3d( pca, group= metabo[,1],
#' fancy= TRUE, bg= "black",
#' axes.color= "white", new= TRUE )
#' @keywords PCA princomp biplot prcomp
#' @name pca3d-package
#' @import rgl
#' @importFrom ellipse ellipse
#' @import graphics
#' @importFrom utils head
#' @importFrom stats cov
NULL
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.